PLplot is a library of C functions that are useful for making scientific plots from programs written in a wide variety of languages. It can be used to create standard x-y plots, semi-log plots, log-log plots, contour plots, 3D plots, shade (gray-scale and color) plots, mesh plots, bar charts, and pie charts. Multiple graphs may be placed on a single page with multiple lines in each graph. Different line styles, widths, and colors are supported. A virtually infinite number of distinct area fill patterns may be used. A variety of output devices and file formats are supported.
FTIDOE is a comprehensive tool for performing the complex process of dynamic energy analysis. This software enables architects and engineers to perform a comprehensive analysis of dynamic heating and cooling loads, simulation of heating and cooling distribution systems, modeling of equipment supplying the required energy, and calculation of the life-cycle costs of owning and operating energy systems for buildings. It can simulate hour-by-hour performance for buildings ranging in size from a small one room residence to a large multi-storied structure for each of the 8760 hours in a year.
GetDP is a general finite element solver using mixed elements to discretize de Rham-type complexes in one, two, and three dimensions. The main feature of GetDP is the closeness between the input data defining discrete problems (written by the user in ASCII data files) and the symbolic mathematical expressions of these problems.
PCP (Pattern Classification Program) is a machine learning program for supervised classification of patterns. It runs in interactive and batch modes, and implements the following machine learning algorithms and methods: k-means clustering, Fisher's linear discriminant, dimension reduction using Singular Value Decomposition, Principal Component Analysis, feature subset selection, Bayes error estimation, parametric classifiers (linear and quadratic), pseudo-inverse linear discriminant, k-Nearest Neighbor method, neural networks, Support Vector Machine algorithm (SVM), model selection for SVM, cross-validation, and bagging (committee) classification.
GSEGYView is a viewer for seismic data in SEG-Y format, its modifications, and many other related formats aimed to store either petroleum exploration data or seismology data. GSEGYView features graphics hardware acceleration via OpenGL for seismic data rendering, wiggle, variable area and variable density seismic traces representation, two-level sorting of seismic traces by arbitratry keys in trace headers, multiple windows for multiple files with separate display parameters, easy seismic section navigation and zoom with mouse wheel support, and more.
APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.
PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include adding a limited number of missing heavy atoms to biomolecular structures, determining side-chain pKas, placing missing hydrogens, optimizing the protein for favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields.